[ome-users] convert .lif file with bfconvert

Fri May 30 15:18:03 BST 2014

Hi Michael,

> "./SCIFIOTestDriver itkSCIFIOImageIOTest/path/to/output_series_0.ome.tiff
/path/to/scifio-test.ome.tiff"

Just a reminder, since you're writing ome.tiff you should have a "-w" flag
at the end of this command. It sounds like you were using -w, just wanted
to clarify for anyone else reading this thread.

> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

 There are two problems here. First, it seems that in SCIFIOImageIO the use
of Bio-Formats is overly aggressive in pulling in all the series, thus the
OutOfMemoryError. If you physically isolate a single series (e.g. delete or
move to another directory series 1-19) the application will run, but we get
another exception (at least on my end):

./SCIFIOTestDriver itkSCIFIOImageIOTest output_series_0.ome.tiff
scifio-test.ome.tiff -w
reader->GetUseStreaming(): 1
done checking streaming usage
ITK test driver caught an ITK exception:

itk::ExceptionObject (0x7ff8838b6ae8)
Location: "unknown"
File:
/Users/mhiner/loci/ITK/build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
Line: 180
Description: itk::ERROR: SCIFIOImageIO(0x7ff8838b4f00): SCIFIOImageIO
exited abnormally. Creating new reader for output_series_0.ome.tiff
log4j:WARN No appenders could be found for logger
(loci.common.services.ServiceFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for
more info.
Exception in thread "main" loci.formats.FormatException: Unmatched UUID:
urn:uuid:b72fe97b-02c9-4029-a876-ca2bae46cbac
    at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:456)
    at loci.formats.FormatReader.setId(FormatReader.java:1244)
    at loci.formats.ImageReader.setId(ImageReader.java:727)
    at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
    at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
    at
loci.scifio.itk.SCIFIOITKBridge.createReader(SCIFIOITKBridge.java:617)
    at
loci.scifio.itk.SCIFIOITKBridge.readImageInfo(SCIFIOITKBridge.java:268)
    at
loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:133)
    at
loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)
    at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)
    at
loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:163)
    at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:688)

I also get this exception when importing with Bio-Formats into Fiji.

As a side note, there are flags for itkSCIFIOImageIOTest that, in theory,
should help the out of memory side:

"-s <n1, n2>" should limit the series read.
"-v <n>" should divide the data into divisions, which might mitigate the
risk of OutOfMemoryErrors.

But neither of these will help the UUID exception. Also, I still got
OutOfMemoryErrors with these, so it was still trying to initialize using
all the series. So I created a new issue
<https://github.com/scifio/scifio-imageio/issues/16> in the SCIFIO-ImageIO
tracker.

Anyway, try importing the bfconvert output into Fiji with Bio-Formats and
let me know if you *don't* get the UUID exception. If you do, then I think
the bfconvert output is just invalid..

Regards,
Mark

On Thu, May 29, 2014 at 12:17 PM, Michael Meuli <michael.meuli at gmail.com>
wrote:

> Hi Mark,
>
> Thanks for the quick response. I can see I was using
> itkSCIFIOImageIOTest the wrong way and it doesn't make sense to use it
> like this.
> If I use the -w flag I get an error in all cases but at the moment I
> don't care as my aim now is to read ome.tiff files with itk.
> I've written a small program (mainly by copy paste from examples /
> https://github.com/michaelmeuli/bactelize) which so far reads the
> multi-channel-z-series.ome.tif file, does a maximum intensity
> projection of one channel and writes a 2D image and it seems to work
> with the multi-channel-z-series.ome.tif but not with the files
> converted with bfconvert.
>
> Expressed with itkSCIFIOImageIOTest:
> "./SCIFIOTestDriver itkSCIFIOImageIOTest
> /path/to/multi-channel-z-series.ome.tif /path/to/scifio-test.ome.tiff"
> doesn't give an error and seems to produce a tiff file of the first
> z-plane, but
> "./SCIFIOTestDriver itkSCIFIOImageIOTest
> /path/to/output_series_0.ome.tiff /path/to/scifio-test.ome.tiff" gives
> an error:
>
> reader->GetUseStreaming(): 1
> done checking streaming usage
> ITK test driver caught an ITK exception:
>
> itk::ExceptionObject (0x2f87680)
> Location: "unknown"
> File:
> /home/michael/Colocalization/ITK-Release-build/Modules/Remote/SCIFIO/src/itkSCIFIOImageIO.cxx
> Line: 180
> Description: itk::ERROR: SCIFIOImageIO(0x2f78970): SCIFIOImageIO
> exited abnormally. Creating new reader for
> /home/michael/bioimage/ome/data/wt-dead-A-ome-tiff/output_series_0.ome.tiff
> log4j:WARN No appenders could be found for logger
> (loci.common.services.ServiceFactory).
> log4j:WARN Please initialize the log4j system properly.
> log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig
> for more info.
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39)
> at java.nio.ByteBuffer.allocate(ByteBuffer.java:312)
> at
> loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:132)
> at
> loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:118)
> at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:532)
> at loci.common.NIOFileHandle.seek(NIOFileHandle.java:254)
> at
> loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:140)
> at loci.formats.tiff.TiffParser.getIFDOffsets(TiffParser.java:308)
> at loci.formats.tiff.TiffParser.getIFDs(TiffParser.java:226)
> at loci.formats.in.MinimalTiffReader.initFile(MinimalTiffReader.java:426)
> at loci.formats.FormatReader.setId(FormatReader.java:1244)
> at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:704)
> at loci.formats.FormatReader.setId(FormatReader.java:1244)
> at loci.formats.ImageReader.setId(ImageReader.java:727)
> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
> at loci.formats.ChannelFiller.setId(ChannelFiller.java:263)
> at loci.scifio.itk.SCIFIOITKBridge.createReader(SCIFIOITKBridge.java:622)
> at loci.scifio.itk.SCIFIOITKBridge.readImageInfo(SCIFIOITKBridge.java:266)
> at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:131)
> at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:108)
> at loci.scifio.itk.SCIFIOITKBridge.waitForInput(SCIFIOITKBridge.java:83)
> at loci.scifio.itk.SCIFIOITKBridge.executeCommand(SCIFIOITKBridge.java:161)
> at loci.scifio.itk.SCIFIOITKBridge.main(SCIFIOITKBridge.java:693)
>
> Best regards
> Michael Meuli
>
>
>
> On 29 May 2014 17:41, Mark Hiner <hiner at wisc.edu> wrote:
> > Hi Michael,
> >
> >
> >> The problem is that ./SCIFIOTestDriver itkSCIFIOImageIOTest
> >> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
> >> (and my little program) throws an exception.
> > ...
> >
> >> How do I use bfconvert the correct way for my case?
> >
> > You used bfconvert correctly to convert your dataset. Just so it's
> clear, if
> > your goal was to produce an OME-TIFF:
> >
> >> /SCIFIOTestDriver itkSCIFIOImageIOTest /path/to/output_series_0.ome.tiff
> >> /path/to/scifiotest.ome.tiff
> >
> > would be unnecessary, as you already have the OME-TIFF output from
> > bfconvert. The itkSCIFIOImageIOTest is an analogous tool to bfconvert
> > written in the Bio-Formats C++ framework. (although comparing the
> outputs of
> > the itkSCIFIOImageIOTest conversion would be a good way to check for
> errors
> > in the conversion process)
> >
> > That said, I believe your conversion failed because the output was
> picked up
> > by the ITK TIFF ImageIO, which I believe only supports 3D data. The
> > itkSCIFIOImageIOTest utility does basically no automation - you have to
> tell
> > it exactly how to run, and because the SCIFIOImageIO is an external
> module
> > it is not prioritized by the ITK format detection framework over internal
> > modules (I'm not sure it's part of the automatic detection framework at
> all,
> > actually). So you need to force the use of the SCIFIOImageIO for writing.
> >
> > If you run:
> >
> >  /SCIFIOTestDriver itkSCIFIOImageIOTest
> >
> > with no arguments from the command line, it will print the usage +
> available
> > flags. The flag you wanted here is "-w"  to write with the SCIFIOImageIO
> > (which will use Bio-Formats, and thus the OME-TIFF writer).
> >
> > So the final syntax is:
> >
> > /SCIFIOTestDriver itkSCIFIOImageIOTest /path/to/output_series_0.ome.tiff
> > /path/to/scifiotest.ome.tiff -w
> >
> > which worked for me locally.
> >
> > Let me know if you have any other questions or issues!
> >
> > Regards,
> > Mark
> >
> > On Thu, May 29, 2014 at 4:40 AM, Michael Meuli <michael.meuli at gmail.com>
> > wrote:
> >>
> >> ./SCIFIOTestDriver itkSCIFIOImageIOTest
> >> /path/to/output_series_0.ome.tiff /path/to/scifiotest.ome.tiff
> >
> >
> >
>
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